[Freesurfer] Pial Surfaces
Dear FreeSurfers I have a problem editing pial surfaces. My pial borders do not include Some important brain parts i.e. amygdala. Can anybody help me? Tnx Sharon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Scripting: Feeding arguments and variables to script?
Hi Graham,
Another way is to generate your TCL on the fly, see below for a simple
example:
- snip -
#!/bin/sh
outdir=/usr/people/johannes/scratch/fssubjects/pictures
mkdir -p $outdir
cd $SUBJECTS_DIR
# put your subjects here
for f in CONTROL*; do
for hemi in lh rh; do
echo scale_brain 1.05
redraw
save_tiff ${outdir}/${f}_thickness_${hemi}.tiff
exit /tmp/prettypic_$$.tcl
tksurfer $f $hemi inflated -overlay $f/surf/${hemi}.thickness -tcl
/tmp/prettypic_$$.tcl
done
done
rm /tmp/prettypic_$$.tcl
- snap -
Cheers,
Johannes
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Re: [Freesurfer] Pial Surfaces
Hi Sharon, the surfaces shouldn't include non-neocortical structures like amygdala. They are modeled separately (in the aseg.mgz file). cheers, Bruce On Mon, 16 Apr 2007, Sharon Ruso wrote: Dear FreeSurfers I have a problem editing pial surfaces. My pial borders do not include Some important brain parts i.e. amygdala. Can anybody help me? Tnx Sharon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Scripting: Feeding arguments and variables to script?
1. When you launch FS from command line and provide a -tcl command to invoke a tcl script, how do you supply arguments to that script (or is that even possible)? There's no way to pass arguments along on the command line, so Bruce's suggestion works best. 3. What assumptions, if any, can a script rely on as to current directory? It will be the same directory from which you started tksurfer. There is a tcl command 'pwd' that will return this. I see most people use an environment variable as the base for paths, unless they want to script to specifically act on something that is in a relative path (like writing a log to the current directory). -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] aseg visualization question
Newer (dev) versions will use $FREESURFER_HOME/FreeSurferColorLUT.txt as the default. On Thu, 12 Apr 2007, Nick Schmansky wrote: This should work: tkmedit good_output brainmask.mgz \ lh.white -aux T1.mgz \ -aux-surface rh.white \ -segmentation mri/aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt On Thu, 2007-04-12 at 16:54 +0100, Morgan Hough wrote: I have a quick question about an error we are getting with FS 3.0.5 when we are using tkmedit as described in the tutorial to display the segmentations overlaid on the T1. tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz The first error seems to regard the new requirement that a color LUT be passed with the segmentation option. If we add tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz tkmeditColorsCMA Then the message reduces to a problem of opening the segmentation file which it says is not in the right .cor format. I assume this is a legacy error message but I am not sure if I need to rename the aseg.mgz file or pass in another option with the file type. Thanks in advance for your time. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] aseg visualization question
Hi, I just want to clear up some confusion about this topic. There is a difference currently between the dev (and stable) versions within the Martinos Center and versions that have been posted for download. Some versions will require you to specify a color table, and also to use the mri/ designation before the aseg.mgz file name. Other versions will not need (and fail if you use) the mri/ designation before the aseg.mgz filename. These versions do not need a color table, as it will read one in by default. It makes the most sense (to me) to continually update the wiki pages to be current with the newest versions, so there are times when certain commands may not be the same as your version - generally nothing drastic. Sorry for any confusion the current documentation has caused. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Doug Greve Sent: Monday, April 16, 2007 7:16 PM To: Nick Schmansky Cc: Morgan Hough; Freesurfer Mailing List Subject: Re: [Freesurfer] aseg visualization question Newer (dev) versions will use $FREESURFER_HOME/FreeSurferColorLUT.txt as the default. On Thu, 12 Apr 2007, Nick Schmansky wrote: This should work: tkmedit good_output brainmask.mgz \ lh.white -aux T1.mgz \ -aux-surface rh.white \ -segmentation mri/aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt On Thu, 2007-04-12 at 16:54 +0100, Morgan Hough wrote: I have a quick question about an error we are getting with FS 3.0.5 when we are using tkmedit as described in the tutorial to display the segmentations overlaid on the T1. tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz The first error seems to regard the new requirement that a color LUT be passed with the segmentation option. If we add tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz tkmeditColorsCMA Then the message reduces to a problem of opening the segmentation file which it says is not in the right .cor format. I assume this is a legacy error message but I am not sure if I need to rename the aseg.mgz file or pass in another option with the file type. Thanks in advance for your time. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert, primary slice direction and resampling
Hi, Can mri_convert work with slice orientation other than axial? My input is sagittal (slices collected from right to left), but when I create files from mri_convert the header reads axial. This is particularly problematic when converting to analyze format from dicoms or another file type because the dimensions of the sagittal slices are applied the transverse plane. Using in_orientation and out_orientation options, the images will display correctly, but the header still reads axial. Can mri_convert subsample an image by retaining every other voxel without interpolating between voxels? Thank you, ~julia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert, primary slice direction and resampling
To more fully explain the road block, this is the output of 'mri_info analyzefile --slicedirection' MatlabRead: readHeader returned NULL WARNING: analyzeRead(): matfile analyzefile.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. - INFO: could not find analyzefile.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in analyzefile.mat file I am running on a Mac. Does this have anything to do with it? I don't have matlab on the mac, but on a windows virtual machine. thanks ~julia On 4/16/07, Julia Hamstra [EMAIL PROTECTED] wrote: Hi, Can mri_convert work with slice orientation other than axial? My input is sagittal (slices collected from right to left), but when I create files from mri_convert the header reads axial. This is particularly problematic when converting to analyze format from dicoms or another file type because the dimensions of the sagittal slices are applied the transverse plane. Using in_orientation and out_orientation options, the images will display correctly, but the header still reads axial. Can mri_convert subsample an image by retaining every other voxel without interpolating between voxels? Thank you, ~julia -- UC Davis Neuroscience Graduate Group The M.I.N.D. Institute - Amaral Lab (916) 703-0376 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
